Merge branch 'master' into pbrubeck/single-source

.github/workflows/build-mac.yml

@@ -50,6 +50,9 @@ jobs:
         run: |
           . ../firedrake_venv/bin/activate
           python -m pytest -v tests/firedrake/regression/ -k "poisson_strong or stokes_mini or dg_advection"
+          # also test for 'problem libraries' (spatialindex and libsupermesh)
+          python -m pytest -v tests/firedrake/regression/test_locate_cell.py
+          python -m pytest -v tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py
         timeout-minutes: 30
       - name: Post-run cleanup
         if: ${{ always() }}

.github/workflows/build.yml

@@ -66,6 +66,7 @@ jobs:
             --mpicxx="$MPICH_DIR"/mpicxx \
             --mpif90="$MPICH_DIR"/mpif90 \
             --mpiexec="$MPICH_DIR"/mpiexec \
+            --mpihome="$MPICH_DIR"/.. \
             --venv-name firedrake_venv \
             --no-package-manager \
             --disable-ssh \

.github/workflows/pip-mac.yml

@@ -68,25 +68,6 @@ jobs:
             --download-superlu_dist
           make
 
-      - name: Install libsupermesh
-        run: |
-          source pip_venv/bin/activate
-          python -m pip install 'rtree>=1.2'
-          cd pip_venv/src
-          git clone https://github.com/firedrakeproject/libsupermesh.git
-          mkdir -p libsupermesh/build
-          cd libsupermesh/build
-          cmake .. \
-            -DBUILD_SHARED_LIBS=ON \
-            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
-            -DMPI_C_COMPILER=/opt/homebrew/bin/mpicc \
-            -DMPI_CXX_COMPILER=/opt/homebrew/bin/mpicxx \
-            -DMPI_Fortran_COMPILER=/opt/homebrew/bin/mpif90 \
-            -DCMAKE_Fortran_COMPILER=/opt/homebrew/bin/mpif90 \
-            -DMPIEXEC_EXECUTABLE=/opt/homebrew/bin/mpiexec
-          make
-          make install
-
       - uses: actions/checkout@v4
         with:
           path: pip_venv/src/firedrake
@@ -118,6 +99,9 @@ jobs:
           cd pip_venv/src/firedrake
           python -m pytest --timeout=1800 -v tests/firedrake/regression \
             -k "poisson_strong or stokes_mini or dg_advection"
+          # also test for 'problem libraries' (spatialindex and libsupermesh)
+          python -m pytest -v tests/firedrake/regression/test_locate_cell.py
+          python -m pytest -v tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py
         timeout-minutes: 30
 
       - name: Cleanup (post)

.github/workflows/pip.yml

@@ -56,25 +56,6 @@ jobs:
         with:
           path: src/firedrake
 
-      - name: Install libsupermesh
-        run: |
-          source pip_venv/bin/activate
-          python -m pip install 'rtree>=1.2'
-          cd pip_venv/src
-          git clone https://github.com/firedrakeproject/libsupermesh.git
-          mkdir -p libsupermesh/build
-          cd libsupermesh/build
-          cmake .. \
-            -DBUILD_SHARED_LIBS=ON \
-            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
-            -DMPI_C_COMPILER="$MPICH_DIR/mpicc" \
-            -DMPI_CXX_COMPILER="$MPICH_DIR/mpicxx" \
-            -DMPI_Fortran_COMPILER="$MPICH_DIR/mpif90" \
-            -DCMAKE_Fortran_COMPILER="$MPICH_DIR/mpif90" \
-            -DMPIEXEC_EXECUTABLE="$MPICH_DIR/mpiexec"
-          make
-          make install
-
       - name: Pip install
         run: |
           source pip_venv/bin/activate

.github/workflows/pyop2.yml

@@ -35,17 +35,6 @@ jobs:
         id: setup-python
         with:
           python-version: ${{ matrix.python-version }}
-          # By default setup-python pollutes the environment in such a way that virtual
-          # environments cannot be used. This prevents us from building libsupermesh because
-          # it relies on having rtree installed into a venv.
-          # https://github.com/actions/setup-python/issues/851
-          # https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#using-update-environment-flag
-          update-environment: false
-
-      - name: Create virtual environment
-        shell: bash
-        run: |
-          ${{ steps.setup-python.outputs.python-path }} -m venv venv
 
       - name: Clone PETSc
         uses: actions/checkout@v4
@@ -65,25 +54,6 @@ jobs:
             --with-fortran-bindings=0
           make
 
-      - name: Install libsupermesh
-        shell: bash
-        run: |
-          source venv/bin/activate
-          python -m pip install 'rtree>=1.2'
-          git clone https://github.com/firedrakeproject/libsupermesh.git
-          mkdir -p libsupermesh/build
-          cd libsupermesh/build
-          cmake .. \
-            -DBUILD_SHARED_LIBS=ON \
-            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
-            -DMPI_C_COMPILER=mpicc \
-            -DMPI_CXX_COMPILER=mpicxx \
-            -DMPI_Fortran_COMPILER=mpif90 \
-            -DCMAKE_Fortran_COMPILER=mpif90 \
-            -DMPIEXEC_EXECUTABLE=mpiexec
-          make
-          make install
-
       - name: Checkout Firedrake
         uses: actions/checkout@v4
         with:
@@ -93,15 +63,13 @@ jobs:
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           python -m pip install -U pip
           python -m pip install -U pytest-timeout
 
       - name: Install PyOP2
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           export CC=mpicc
           export HDF5_DIR="$PETSC_DIR/$PETSC_ARCH"
           export HDF5_MPI=ON
@@ -111,15 +79,13 @@ jobs:
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           pytest --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/tsfc
         timeout-minutes: 10
 
       - name: Run PyOP2 tests
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           pytest -m "not parallel" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
           mpiexec -n 2 --oversubscribe pytest -m "parallel[2]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
           mpiexec -n 3 --oversubscribe pytest -m "parallel[3]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2

docker/Dockerfile.complex

@@ -18,5 +18,6 @@ RUN bash -c "python3 firedrake-install \
     --mpicxx=$MPICH_DIR/mpicxx \
     --mpif90=$MPICH_DIR/mpif90 \
     --mpiexec=$MPICH_DIR/mpiexec \
+    --mpihome=$MPICH_DIR/.. \
     --slepc \
     --documentation-dependencies"

docker/Dockerfile.vanilla

@@ -16,4 +16,5 @@ RUN bash -c "python3 firedrake-install \
     --mpicc=$MPICH_DIR/mpicc \
     --mpicxx=$MPICH_DIR/mpicxx \
     --mpif90=$MPICH_DIR/mpif90 \
-    --mpiexec=$MPICH_DIR/mpiexec"
+    --mpiexec=$MPICH_DIR/mpiexec \
+    --mpihome=$MPICH_DIR/.."

docs/source/download.rst

@@ -241,7 +241,6 @@ Requirements
 * An activated virtual environment.
 * All the system requirements listed in :ref:`system-requirements`.
 * A Firedrake-compatible PETSc installation (using our `fork of PETSc <https://github.com/firedrakeproject/petsc.git>`_). The set of flags passed to PETSc can be retrieved by passing the command ``--show-petsc-configure-options`` to ``firedrake-install``.
-* `libsupermesh <https://github.com/firedrakeproject/libsupermesh.git>`_ to be installed inside the virtual environment (see `here <https://github.com/firedrakeproject/firedrake/blob/master/.github/workflows/pip.yml>`_ for an example of how to do this).
 *  The following environment variables to be set:
 
   * ``PETSC_DIR`` and ``PETSC_ARCH`` to point to the correct location for the PETSc installation.

docs/source/firedrake_usa_25.rst

@@ -27,13 +27,13 @@ The conference will begin with a tutorial session on the morning of 28 February
 Conference venue
 ----------------
 
-The conference will take place in the Bill Daniel Student Center in Room 202 in the heart of the Baylor campus.
+The conference will take place in the Bill Daniel Student Center in Room 202 in the heart of the Baylor campus.  A `campus map <https://map.baylor.edu/>`__ is available online, and both Apple Maps and Google Maps accurately locate the Bill Daniel Student Center.  
 
 
 Accommodation
 -------------
 
-We will be reserving a room block in a hotel near campus.  More information to follow.
+We have reserved a block of hotel rooms at SpringHill Suites Waco, about a 15 minute walk from the Bill Daniel Student Center.  Follow `this link <https://www.marriott.com/event-reservations/reservation-link.mi?id=1734040121673&key=GRP&guestreslink2=true&app=resvlink/>`__ to hold your room.  The group rate is only available until 20 January 2025.
 
 
 Conference dinner
@@ -53,9 +53,9 @@ The registration fees are as follows:
    :widths: 25 50
    :header-rows: 0
 
-   * - Student
+   * - Student:
      - $50
-   * - Non-student
+   * - Non-student:
      - $200
 
 The `SIAM Texas-Louisiana Section <https://www.siam.org/get-involved/connect-with-a-community/sections/siam-texas-louisiana-section/>`__ is providing some support for students currently attending universities in Texas or Louisiana to attend.
@@ -66,7 +66,7 @@ Conference registration is coming soon.
 Abstract submission
 -------------------
 
-Abstract submission will open soon via Easy Chair.
+Abstracts can be submitted `via EasyChair <https://easychair.org/conferences/?conf=firedrakeusa25>`__.
 
 
 
@@ -79,17 +79,11 @@ The conference has been kindly supported by the SIAM TX-LA Section and EPSRC.
 Travel to Waco
 --------------
 
-* By air
+* By air:  Waco has a small airport.  There is daily service between Waco and Dallas/Fort Worth International Airport via American Airlines.  
 
-   Waco has a small airport.  There is daily service between Waco and Dallas/Fort Worth International Airport via American Airlines.  
+* By ground:  We are less than two hours by car from the Dallas and Austin airports, and just under three hours from Bush Intercontinental Airport in Houston.  Additionally, Waco is reachable by bus services such as Greyhound and FlixBus.
 
-* By ground
-
-  We are less than two hours by car from the Dallas and Austin airports, and just under three hours from Bush Intercontinental Airport in Houston.  Additionally, Waco is reachable by bus services such as Greyhound and FlixBus.
-
-* Parking on campus
-
-  Baylor has plenty of visitor parking for your personal or rental vehicle, but conslut `these instructions <https://dps.web.baylor.edu/parking-transportation/visitors>__` and make sure to `register your vehicle <https://dps.web.baylor.edu/parking-transportation/visitors/visitor-parking-permit>__`.
+* Parking on campus:  Baylor has plenty of visitor parking for your personal or rental vehicle, but consult `these instructions <https://dps.web.baylor.edu/parking-transportation/visitors>`__ and make sure to `register your vehicle <https://dps.web.baylor.edu/parking-transportation/visitors/visitor-parking-permit>`__.
 
 
 

docs/source/parallelism.rst

@@ -45,11 +45,12 @@ firedrake installer to use it, by running:
 
 .. code-block:: shell
 
-   python3 firedrake-install --mpiexec=mpiexec --mpicc=mpicc --mpicxx=mpicxx --mpif90=mpif90
+   python3 firedrake-install --mpiexec=mpiexec --mpicc=mpicc --mpicxx=mpicxx --mpif90=mpif90 --mpihome mpihome
 
 where ``mpiexec``, ``mpicc``, ``mpicxx``, and ``mpif90`` are the
 commands to run an MPI job and to compile C, C++, and Fortran 90 code,
-respectively.
+respectively. ``mpihome`` is an extra variable that must point to the
+root directory of the MPI installation (e.g. ``/usr`` or ``/opt/mpich``).
 
 Printing in parallel
 ====================

firedrake/cython/dmcommon.pyx

@@ -3358,7 +3358,7 @@ def make_global_numbering(PETSc.Section lsec, PETSc.Section gsec):
     cdef:
         PetscInt c, cc, p, pStart, pEnd, dof, cdof, loff, goff
         np.ndarray val
-        PetscInt *dof_array = NULL
+        const PetscInt *dof_array = NULL
 
     val = np.empty(lsec.getStorageSize(), dtype=IntType)
     pStart, pEnd = lsec.getChart()

firedrake/interpolation.py

@@ -1092,8 +1092,7 @@ def _interpolator(V, tensor, expr, subset, arguments, access, bcs=None):
     # interpolation) we have to pass the finat element we construct
     # here. Ideally we would only pass the UFL element through.
     kernel = compile_expression(cell_set.comm, expr, to_element, V.ufl_element(),
-                                domain=source_mesh, parameters=parameters,
-                                log=PETSc.Log.isActive())
+                                domain=source_mesh, parameters=parameters)
     ast = kernel.ast
     oriented = kernel.oriented
     needs_cell_sizes = kernel.needs_cell_sizes
@@ -1221,10 +1220,9 @@ def _interpolator(V, tensor, expr, subset, arguments, access, bcs=None):
                                   f"firedrake-tsfc-expression-kernel-cache-uid{os.getuid()}")
 
 
-def _compile_expression_key(comm, expr, to_element, ufl_element, domain, parameters, log):
+def _compile_expression_key(comm, expr, to_element, ufl_element, domain, parameters):
     """Generate a cache key suitable for :func:`tsfc.compile_expression_dual_evaluation`."""
-    key = hash_expr(expr), hash(ufl_element), utils.tuplify(parameters), log
-    return key
+    return (hash_expr(expr), hash(ufl_element), utils.tuplify(parameters))
 
 
 @memory_and_disk_cache(

firedrake/parloops.py

@@ -171,7 +171,7 @@ def par_loop(kernel, measure, args, kernel_kwargs=None, **kwargs):
       domain = '{[i]: 0 <= i < A.dofs}'
       instructions = '''
       for i
-          A[i] = max(A[i], B[0])
+          A[i] = fmax(A[i], B[0])
       end
       '''
       par_loop((domain, instructions), dx, {'A' : (A, RW), 'B': (B, READ)})

firedrake/preconditioners/pmg.py

@@ -530,7 +530,7 @@ def coarsen_bc_value(self, bc, cV):
 
 def prolongation_transfer_kernel_action(Vf, expr):
     to_element = create_element(Vf.ufl_element())
-    kernel = compile_expression_dual_evaluation(expr, to_element, Vf.ufl_element(), log=PETSc.Log.isActive())
+    kernel = compile_expression_dual_evaluation(expr, to_element, Vf.ufl_element())
     coefficients = extract_numbered_coefficients(expr, kernel.coefficient_numbers)
     if kernel.needs_external_coords:
         coefficients = [Vf.mesh().coordinates] + coefficients

firedrake/slate/slac/compiler.py

@@ -237,4 +237,4 @@ def gem_to_loopy(gem_expr, var2terminal, scalar_type):
 
     # Part B: impero_c to loopy
     output_arg = OutputKernelArg(output_loopy_arg)
-    return generate_loopy(impero_c, args, scalar_type, "slate_loopy", [], log=PETSc.Log.isActive()), output_arg
+    return generate_loopy(impero_c, args, scalar_type, "slate_loopy", []), output_arg

firedrake/supermeshing.py

@@ -1,7 +1,8 @@
 # Code for projections and other fun stuff involving supermeshes.
 import firedrake
 import ctypes
-import sys
+import pathlib
+import libsupermesh
 from firedrake.cython.supermeshimpl import assemble_mixed_mass_matrix as ammm, intersection_finder
 from firedrake.mg.utils import get_level
 from firedrake.petsc import PETSc
@@ -428,7 +429,8 @@ def likely(cell_A):
         "complex_mode": 1 if complex_mode else 0
     }
 
-    dirs = get_petsc_dir() + (sys.prefix, )
+    libsupermesh_dir = pathlib.Path(libsupermesh.get_include()).parent.absolute()
+    dirs = get_petsc_dir() + (libsupermesh_dir,)
     includes = ["-I%s/include" % d for d in dirs]
     libs = ["-L%s/lib" % d for d in dirs]
     libs = libs + ["-Wl,-rpath,%s/lib" % d for d in dirs] + ["-lpetsc", "-lsupermesh"]

firedrake/tsfc_interface.py

@@ -53,8 +53,8 @@
 )
 
 
-def tsfc_compile_form_hashkey(form, prefix, parameters, interface, diagonal, log):
-    # Drop prefix as it's only used for naming and log
+def tsfc_compile_form_hashkey(form, prefix, parameters, interface, diagonal):
+    # Drop prefix as it's only used for naming
     return default_parallel_hashkey(form.signature(), prefix, parameters, interface, diagonal)
 
 
@@ -94,7 +94,7 @@ def __init__(
         """
         tree = tsfc_compile_form(form, prefix=name, parameters=parameters,
                                  interface=interface,
-                                 diagonal=diagonal, log=PETSc.Log.isActive())
+                                 diagonal=diagonal)
         kernels = []
         for kernel in tree:
             # Individual kernels do not have to use all of the coefficients